data_9EMA
#
_model_server_result.job_id            YYpHrL_7tVLpqbUlCP3qbA 
_model_server_result.datetime_utc      '2025-07-07 22:25:49' 
_model_server_result.server_version    0.9.12 
_model_server_result.query_name        ligand 
_model_server_result.source_id         pdb-bcif 
_model_server_result.entry_id          9ema 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":502}' 
#
_entry.id    9EMA 
#
_exptl.entry_id    9EMA 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              573.055 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            5-chloranyl-2-ethoxy-4-fluoranyl-~{N}-[4-[[3-(methoxymethyl)-1-oxidanylidene-6,7-dihydro-5~{H}-pyrazolo[1,2-a][1,2]benzodiazepin-2-yl]amino]-2,2-dimethyl-4-oxidanylidene-butyl]benzamide 
_entity.pdbx_number_of_molecules    3 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1 
#
_pdbx_struct_oper_list.id                    1 
_pdbx_struct_oper_list.type                  'identity operation' 
_pdbx_struct_oper_list.name                  1_555 
_pdbx_struct_oper_list.symmetry_operation    x,y,z 
_pdbx_struct_oper_list.matrix[1][1]          1 
_pdbx_struct_oper_list.matrix[1][2]          0 
_pdbx_struct_oper_list.matrix[1][3]          0 
_pdbx_struct_oper_list.matrix[2][1]          0 
_pdbx_struct_oper_list.matrix[2][2]          1 
_pdbx_struct_oper_list.matrix[2][3]          0 
_pdbx_struct_oper_list.matrix[3][1]          0 
_pdbx_struct_oper_list.matrix[3][2]          0 
_pdbx_struct_oper_list.matrix[3][3]          1 
_pdbx_struct_oper_list.vector[1]             0 
_pdbx_struct_oper_list.vector[2]             0 
_pdbx_struct_oper_list.vector[3]             0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 H N N 
? 4 J N N 
? 4 L N N 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_PDB_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
metalc ? metalc1 G O3G ATP . A ATP 501 1_555 Q MG MG . F MG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? 
metalc ? metalc2 G O3B ATP . A ATP 501 1_555 Q MG MG . F MG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.866 ? 
metalc ? metalc3 G O1A ATP . A ATP 501 1_555 Q MG MG . F MG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? 
metalc ? metalc4 D OG1 THR 102 D THR 84 1_555 N MG MG . D MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? 
metalc ? metalc5 M O1G ATP . D ATP 801 1_555 N MG MG . D MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? 
metalc ? metalc6 M O2B ATP . D ATP 801 1_555 N MG MG . D MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? 
metalc ? metalc7 E OG1 THR 102 E THR 84 1_555 P MG MG . E MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? 
metalc ? metalc8 O O1G ATP . E ATP 801 1_555 P MG MG . E MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? 
metalc ? metalc9 O O2B ATP . E ATP 801 1_555 P MG MG . E MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? 
metalc ? metalc10 O O1A ATP . E ATP 801 1_555 P MG MG . E MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.939 ? 
metalc ? metalc11 F OG1 THR 102 F THR 84 1_555 S MG MG . F MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
metalc ? metalc12 F OE2 GLU 335 F GLU 317 1_555 Q MG MG . F MG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? 
metalc ? metalc13 R O1G ATP . F ATP 802 1_555 S MG MG . F MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.49 ? 
metalc ? metalc14 R O2B ATP . F ATP 802 1_555 S MG MG . F MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? 
metalc ? metalc15 R O1A ATP . F ATP 802 1_555 S MG MG . F MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.859 ? 
#
_chem_comp.formula           'C29 H34 Cl F N4 O5' 
_chem_comp.formula_weight    573.055 
_chem_comp.id                A1H5V 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              5-chloranyl-2-ethoxy-4-fluoranyl-~{N}-[4-[[3-(methoxymethyl)-1-oxidanylidene-6,7-dihydro-5~{H}-pyrazolo[1,2-a][1,2]benzodiazepin-2-yl]amino]-2,2-dimethyl-4-oxidanylidene-butyl]benzamide 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
loop_
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.comp_id
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_ordinal
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_aromatic_flag
C37 C38 A1H5V doub 1 n y 
C37 C36 A1H5V sing 2 n y 
C38 C39 A1H5V sing 3 n y 
C36 C35 A1H5V doub 4 n y 
C39 C34 A1H5V doub 5 n y 
C35 C34 A1H5V sing 6 n y 
C35 C33 A1H5V sing 7 n n 
C34 N29 A1H5V sing 8 n n 
O40 C28 A1H5V doub 9 n n 
C33 C32 A1H5V sing 10 n n 
N29 C28 A1H5V sing 11 n n 
N29 N30 A1H5V sing 12 n n 
C19 C18 A1H5V sing 13 n n 
C28 C05 A1H5V sing 14 n n 
C32 C31 A1H5V sing 15 n n 
F22 C21 A1H5V sing 16 n n 
N30 C31 A1H5V sing 17 n n 
N30 C04 A1H5V sing 18 n n 
C20 C21 A1H5V doub 19 n y 
C20 C16 A1H5V sing 20 n y 
C18 O17 A1H5V sing 21 n n 
C21 C23 A1H5V sing 22 n y 
O17 C16 A1H5V sing 23 n n 
C05 C04 A1H5V doub 24 n n 
C05 N06 A1H5V sing 25 n n 
C16 C15 A1H5V doub 26 n y 
C04 C03 A1H5V sing 27 n n 
O27 C07 A1H5V doub 28 n n 
N06 C07 A1H5V sing 29 n n 
C07 C08 A1H5V sing 30 n n 
C23 CL24 A1H5V sing 31 n n 
C23 C25 A1H5V doub 32 n y 
C15 C25 A1H5V sing 33 n y 
C15 C14 A1H5V sing 34 n n 
C03 O02 A1H5V sing 35 n n 
C08 C09 A1H5V sing 36 n n 
O02 C01 A1H5V sing 37 n n 
N13 C14 A1H5V sing 38 n n 
N13 C12 A1H5V sing 39 n n 
C14 O26 A1H5V doub 40 n n 
C12 C09 A1H5V sing 41 n n 
C09 C11 A1H5V sing 42 n n 
C09 C10 A1H5V sing 43 n n 
C01 H1 A1H5V sing 44 n n 
C01 H2 A1H5V sing 45 n n 
C01 H3 A1H5V sing 46 n n 
C03 H4 A1H5V sing 47 n n 
C03 H5 A1H5V sing 48 n n 
N06 H6 A1H5V sing 49 n n 
C08 H7 A1H5V sing 50 n n 
C08 H8 A1H5V sing 51 n n 
C10 H9 A1H5V sing 52 n n 
C10 H10 A1H5V sing 53 n n 
C10 H11 A1H5V sing 54 n n 
C11 H12 A1H5V sing 55 n n 
C11 H13 A1H5V sing 56 n n 
C11 H14 A1H5V sing 57 n n 
C12 H15 A1H5V sing 58 n n 
C12 H16 A1H5V sing 59 n n 
N13 H17 A1H5V sing 60 n n 
C18 H18 A1H5V sing 61 n n 
C18 H19 A1H5V sing 62 n n 
C19 H20 A1H5V sing 63 n n 
C19 H21 A1H5V sing 64 n n 
C19 H22 A1H5V sing 65 n n 
C20 H23 A1H5V sing 66 n n 
C25 H24 A1H5V sing 67 n n 
C31 H25 A1H5V sing 68 n n 
C31 H26 A1H5V sing 69 n n 
C32 H27 A1H5V sing 70 n n 
C32 H28 A1H5V sing 71 n n 
C33 H29 A1H5V sing 72 n n 
C33 H30 A1H5V sing 73 n n 
C36 H31 A1H5V sing 74 n n 
C37 H32 A1H5V sing 75 n n 
C38 H33 A1H5V sing 76 n n 
C39 H34 A1H5V sing 77 n n 
#
_atom_sites.entry_id                     9EMA 
_atom_sites.fract_transf_matrix[1][1]    1 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    1 
_atom_sites.fract_transf_matrix[2][3]    0 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    1 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
loop_
_pdbx_nonpoly_scheme.asym_id
_pdbx_nonpoly_scheme.entity_id
_pdbx_nonpoly_scheme.mon_id
_pdbx_nonpoly_scheme.pdb_strand_id
_pdbx_nonpoly_scheme.ndb_seq_num
_pdbx_nonpoly_scheme.pdb_seq_num
_pdbx_nonpoly_scheme.auth_seq_num
_pdbx_nonpoly_scheme.pdb_mon_id
_pdbx_nonpoly_scheme.auth_mon_id
_pdbx_nonpoly_scheme.pdb_ins_code
G 3 ATP A 1 501 500 ATP ATP . 
H 4 A1H5V A 1 502 503 A1H5V CB6 . 
I 3 ATP B 1 500 500 ATP ATP . 
J 4 A1H5V B 1 501 501 A1H5V CB6 . 
K 3 ATP C 1 501 500 ATP ATP . 
L 4 A1H5V C 1 502 502 A1H5V CB6 . 
M 3 ATP D 1 801 500 ATP ATP . 
N 5 MG D 1 802 501 MG MG . 
O 3 ATP E 1 801 500 ATP ATP . 
P 5 MG E 1 802 501 MG MG . 
Q 5 MG F 1 801 501 MG MG . 
R 3 ATP F 1 802 500 ATP ATP . 
S 5 MG F 1 803 501 MG MG . 
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_seq_id
_atom_site.label_alt_id
_atom_site.pdbx_PDB_ins_code
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.auth_seq_id
_atom_site.auth_asym_id
_atom_site.pdbx_PDB_model_num
HETATM 1 CL CL24 A1H5V . . . H 4 151.758 120.132 121.1 1 22.41 ? CL24 A1H5V 502 A 1 
HETATM 2 C C01 A1H5V . . . H 4 155.276 131.237 122.817 1 25.14 ? C01 A1H5V 502 A 1 
HETATM 3 O O02 A1H5V . . . H 4 154.641 131.23 121.564 1 35.39 ? O02 A1H5V 502 A 1 
HETATM 4 C C03 A1H5V . . . H 4 154.122 132.469 121.187 1 21.86 ? C03 A1H5V 502 A 1 
HETATM 5 C C04 A1H5V . . . H 4 153.515 132.314 119.793 1 19.7 ? C04 A1H5V 502 A 1 
HETATM 6 C C05 A1H5V . . . H 4 152.221 131.546 119.407 1 19.37 ? C05 A1H5V 502 A 1 
HETATM 7 N N06 A1H5V . . . H 4 151.317 130.837 120.273 1 17.43 ? N06 A1H5V 502 A 1 
HETATM 8 C C07 A1H5V . . . H 4 151.447 129.421 120.447 1 19.59 ? C07 A1H5V 502 A 1 
HETATM 9 C C08 A1H5V . . . H 4 150.469 128.687 121.356 1 19.95 ? C08 A1H5V 502 A 1 
HETATM 10 C C09 A1H5V . . . H 4 150.986 128.455 122.764 1 20.39 ? C09 A1H5V 502 A 1 
HETATM 11 C C10 A1H5V . . . H 4 149.933 127.692 123.566 1 18.68 ? C10 A1H5V 502 A 1 
HETATM 12 C C11 A1H5V . . . H 4 151.267 129.786 123.449 1 16.93 ? C11 A1H5V 502 A 1 
HETATM 13 C C12 A1H5V . . . H 4 152.278 127.646 122.692 1 20.47 ? C12 A1H5V 502 A 1 
HETATM 14 N N13 A1H5V . . . H 4 152.128 126.591 121.719 1 16.65 ? N13 A1H5V 502 A 1 
HETATM 15 C C14 A1H5V . . . H 4 151.745 125.266 122.128 1 15.88 ? C14 A1H5V 502 A 1 
HETATM 16 C C15 A1H5V . . . H 4 151.601 124.168 121.092 1 19.96 ? C15 A1H5V 502 A 1 
HETATM 17 C C16 A1H5V . . . H 4 151.368 124.469 119.758 1 20.91 ? C16 A1H5V 502 A 1 
HETATM 18 O O17 A1H5V . . . H 4 151.24 125.795 119.33 1 31.17 ? O17 A1H5V 502 A 1 
HETATM 19 C C18 A1H5V . . . H 4 150.757 125.947 118.02 1 14.41 ? C18 A1H5V 502 A 1 
HETATM 20 C C19 A1H5V . . . H 4 149.562 126.891 118.03 1 21.13 ? C19 A1H5V 502 A 1 
HETATM 21 C C20 A1H5V . . . H 4 151.247 123.446 118.847 1 15.92 ? C20 A1H5V 502 A 1 
HETATM 22 C C21 A1H5V . . . H 4 151.37 122.139 119.268 1 13.16 ? C21 A1H5V 502 A 1 
HETATM 23 C C23 A1H5V . . . H 4 151.606 121.833 120.588 1 15.44 ? C23 A1H5V 502 A 1 
HETATM 24 C C25 A1H5V . . . H 4 151.722 122.854 121.505 1 20.54 ? C25 A1H5V 502 A 1 
HETATM 25 O O26 A1H5V . . . H 4 151.559 125.025 123.267 1 25.58 ? O26 A1H5V 502 A 1 
HETATM 26 O O27 A1H5V . . . H 4 152.306 128.838 119.881 1 17.29 ? O27 A1H5V 502 A 1 
HETATM 27 C C28 A1H5V . . . H 4 152.086 131.715 117.862 1 16.86 ? C28 A1H5V 502 A 1 
HETATM 28 N N29 A1H5V . . . H 4 153.227 132.501 117.465 1 20.22 ? N29 A1H5V 502 A 1 
HETATM 29 N N30 A1H5V . . . H 4 154.008 132.831 118.53 1 23.74 ? N30 A1H5V 502 A 1 
HETATM 30 C C31 A1H5V . . . H 4 155.253 133.618 118.621 1 19.17 ? C31 A1H5V 502 A 1 
HETATM 31 C C32 A1H5V . . . H 4 155.034 135.072 118.239 1 17.28 ? C32 A1H5V 502 A 1 
HETATM 32 C C33 A1H5V . . . H 4 153.905 135.277 117.242 1 18.87 ? C33 A1H5V 502 A 1 
HETATM 33 C C34 A1H5V . . . H 4 153.67 133.023 116.141 1 21.68 ? C34 A1H5V 502 A 1 
HETATM 34 C C35 A1H5V . . . H 4 153.991 134.345 116.014 1 18.14 ? C35 A1H5V 502 A 1 
HETATM 35 C C36 A1H5V . . . H 4 154.404 134.85 114.758 1 17.83 ? C36 A1H5V 502 A 1 
HETATM 36 C C37 A1H5V . . . H 4 154.476 133.99 113.665 1 17.05 ? C37 A1H5V 502 A 1 
HETATM 37 C C38 A1H5V . . . H 4 154.141 132.637 113.8 1 18.39 ? C38 A1H5V 502 A 1 
HETATM 38 C C39 A1H5V . . . H 4 153.735 132.14 115.03 1 20.99 ? C39 A1H5V 502 A 1 
HETATM 39 O O40 A1H5V . . . H 4 151.233 131.285 117.161 1 28.87 ? O40 A1H5V 502 A 1 
HETATM 40 F F22 A1H5V . . . H 4 151.256 121.148 118.366 1 19.56 ? F22 A1H5V 502 A 1 
#
_model_server_stats.io_time_ms              102 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    146 
_model_server_stats.query_time_ms           391 
_model_server_stats.encode_time_ms          52 
_model_server_stats.element_count           40 
#